Lost Soul
by August08
Summary: They always believed there were only four of them. The only ones of their kind. However, when a mysterious figure bearing an uncanny resemblance to one of them is seen committing horrendous crimes, it throws everything the brothers know into a wild whirlwind of confusion and panic. But, Mikey sees an opportunity to help. And, maybe, he'll even gain another brother in the process.
1. Chapter 1

**A/N** : I was gifted with the Teenage Mutant Ninja Turtles: Out of the Shadows movie on DVD for Christmas, and needless to say, I've watched it that many times I almost have it memorized (almost). Can anyone say...addicted? *blushes* Anyway, I usually write TMNT stories in the 2003 universe, but I've grown to love the 2014 Turtles so much that I've decided to try my hand at a story set in that universe. I hope you enjoy the story.

Reviews and constructive criticism are always appreciated as they help me grow as a writer. Flames and negativity never helped anything (just watch the news. The world is screwed up enough as it is, please don't add to it). If you don't like the story, simply...don't read it.

 **Disclaimer** : I own nothing associated with TMNT, they belong to their respective owners. I only own the OC. The rest I'm just burrowing for fun.

* * *

 _He stood on the edge of the Chrysler Building. The wind whipped at his mask tails. Blue eyes gazed out over the sunlit metropolis below him. What was he doing out during the day? He was going to be seen. Leonardo reached for the radio pinned to his shoulder to call the others. He looked down when he found it wasn't there. His radio and his weapons were gone. Leonardo gasped in shock and surprise. He was out in the open defenseless._

 _The building suddenly shook. Leonardo caught himself before he could fall. He looked down to see giant metal panels zooming underneath him. He turned his eyes upward, heart dropping like a brick into his stomach at the sight of the Technodrome. It wasn't possible. They had sent the warship back through the portal. They defeated Krang._

 _"Leo!" came a terrified scream._

 _Leonardo's head snapped around. His eyes landed on a figure hanging from another ledge. He cried out when he realized it was April. Leonardo made a move towards her, but then he heard his name coming from a different direction. He looked over his shoulder. His brothers were fighting against Krang on the still constructing Technodrome. They were getting clobbered. Leonardo's eyes widened in horror when Raphael was thrown off the platform._

 _"Raph!" the blue masked leader cried as he watched his brother plummet towards the earth._

 _"Leo!" April screamed again._

 _Leonardo looked between April and his brothers._

 _"Which one? Which one?" a deep, haunting voice whispered._

 _Leonardo turned around. The breath left his lungs when he beheld the turtle before him. At first glance he looked like Raphael. Same build, same facial structure. But, his eyes were wrong. They were a dark, fathomless black. The turtle wore no mask, only a pair of tattered pants._

 _"Can only save one, fearless leader," the turtle said. "Which is it gonna be?"_

 _"Who are you?" Leonardo asked, his voice no more than a whisper._

 _The turtle gave him a dark stare. "Me?" he asked, stepping forward. The building seemed to vibrate with his powerful gait. "I'm the one you couldn't save. Just like you can't save them."_

 _"Leo!" April's voice rang with the voices of his brothers._

 _"Can't save us all, fearless leader," the turtle said. "So, choose!"_

 _Leonardo cried out as the turtle pushed him backwards. He was falling for a brief moment before his shell hit a piece of the Technodrome._

Blue eyes shot open, breath coming out in raspy gasps. Leonardo sat up in bed, his skin covered in a cold sweat. He put a hand to his chest. His heart pounded painfully against his ribs. Leonardo put a hand over his eyes. He could feel his hand trembling. He jumped and cried out when the bedroom door suddenly burst open. Leonardo's head snapped up, his eyes wide. Raphael stood in the doorway, his own eyes wide and fearful.

"You okay, bro?" the red masked turtle asked.

"I'm fine," Leonardo replied. "Why do you ask?"

Raphael moved towards the bed. "You were cryin' out in your sleep," he answered.

"Was I?" Leonardo asked, feeling his face burn with embarrassment. "I didn't realize."

His heart continued to pound, but now it hammered with relief. To see Raphael here, in front of him, living and breathing, it was a welcomed relief to know that what he had seen had just been a dream. The mattress shifted as Raphael sat down on the bed.

"Who was it, this time?"

Leonardo looked up at his brother, eyes questioning. However, he could see in his sibling's eyes that Raphael already knew the answer. Leonardo swallowed thickly and looked away again. He could still hear himself cry out his hot-headed brother's name.

"You'd think something like that wouldn't affect you," Raphael commented. "After all, we should be used to saving the city from power crazed maniacs."

Leonardo's eyes drifted upward. Raphael's face was haunted, his amber eyes distant and locked on the floor.

"You'd think," Leonardo muttered.

They fell into a heavy silence. Leonardo thought he was going to suffocate.

"I still have nightmares about the first time we faced off against Shredder," Raphael suddenly spoke. "Seeing you, Mikey and Donnie in those cages...your blood being syphoned out of you...but, I never make it. Mikey and Donnie are already dead by the time I get there. I pull you free, but only to have you die in my arms a short time after."

Leonardo stared at his brother in stunned shock. He never knew Raphael had nightmares. He was always so guarded. Burying his feelings underneath a wall of anger that all anyone ever saw was the rage. Sometimes Leonardo shamefully forgot that Raphael had other feelings besides anger. However, his brother so rarely let them show that it was easy to forget.

"What we do...it's not easy," Raphael continued. "It leaves scars...scars that no one can see, even when the visible ones fade."

He quickly glanced over at his brother, cleared his throat and abruptly stood up, catching Leonardo off guard. The blue masked brother didn't miss the glistening in his brother's eyes.

"Anyway, I'm glad you're okay, Leo," Raphael said.

He headed for the door before Leonardo could say anything. The leader sat in bed, mind reeling. What had just happened? Did Raphael...open up to him? That never happened. Raphael never opened up to anyone, not even Splinter. There was probably no one in their small circle that knew what truly went on inside Raphael's mind. And, there probably never would be.

From downstairs, Leonardo could hear a door opening and excited laughter. Donatello and Michelangelo were home. Leonardo pushed back the blankets and got out of bed. He grabbed his mask and swords and headed downstairs, tying the mask around his eyes as he went.

"Those dudes were such pushovers," Michelangelo was saying as Leonardo descended the stairs into the main area of the lair.

"Training go okay?" Leonardo asked.

"I can't believe Master Splinter gave us permission to share our knowledge of martial arts with the police," Donatello said.

"The Foot clan is still a threat," Leonardo told him. "And we can't always be there as backup. The police need the proper training to handle ninjas."

"But, still. We're working with humans, dude," Michelangelo said. "It's like...a dream come true."

Leonardo smiled at his little brother's enthusiasm. He was still wrapping his head around it himself. However, the golden key that hung on the side of his mirror was proof that they had earned the trust of at least the police department.

"Where's Raph?" Donatello asked, looking around the lair. "I thought he stayed home."

Leonardo frowned and looked around the lair. "He did. I was just talking to him. He must have gone out just before you got here."

"Well, in any case, you two missed out on a great day," Donatello said. "Or...technically a great night."

Leonardo smiled. "Next time," he said.

Donatello and Michelangelo headed off to their own corners of the lair. Leonardo headed for his training platform in the middle of the lair. He unsheathed his katanas and started his katas. He hoped that Raphael was okay. There seemed to have been something else that was weighing on his mind. Leonardo felt a slight hope rise in his chest that maybe Raphael would come to him if he needed to talk. He knew that they rarely saw eye to eye, but they were still brothers. They could do more together than just fight with each other.

 _Come home safely, Raph,_ Leonardo silently prayed.

* * *

Raphael ran his hands over his face as the warm summer air danced over his skin. He breathed in deep, trying to clear the cobwebs from his mind. His confession about his nightmares had left a weird feeling in his stomach. He had never opened up to anyone about anything. Admitting to his brother that he had those kinds of dreams was like confessing his deepest, darkest feelings.

Raphael leaned up against the edge of the roof and gazed out over the brightly lit city far below him. A tired smile crossed his lips. Man, he loved this city. He didn't understand why anyone would want to do it harm. His smile faded as he thought about his most recent string of nightmares.

He was always standing in a mirrored room. Nothing but his reflection in all directions. There was nothing special about it, it was just his reflection. Then, as soon as he blinked, it changed. His gear vanished, his mask disappeared, and his eyes turned from amber to soulless black. And then, like a phantom, the reflection stepped out of the mirror. The look in the other turtle's eyes was enough to turn Raphael's blood to ice.

"Who are you?" Raphael whispered in horror.

"The one you left behind," the reflection hissed back in his voice, but it wasn't his voice, it was deeper, darker. "You think you're so tough? So honorable? So did they."

The other turtle then proceeded to smash the four mirrored walls surrounding them. When the glass shattered to the floor a different member of his family was lying lifeless behind it.

"You did this," the other turtle seethed venomously. "They'll all fall by your hand. Your brothers...father...even those three humans you care so much about."

"Raph," would then come a choking gasp.

The dream would end as he looked down at the lifeless bodies of Vern, April and Casey.

Raphael shook his head, banishing the memory. "It's not gonna happen. It's not gonna happen," he repeated to himself. "You're not gonna kill your family."

But, how could he be so sure? It was no secret he had rage issues. What was to stop him from hurting one or more of the others when he lost himself? He had often wondered how hard it would be to take Leonardo out when he was in one of his rage filled hazes. Of course, he always had someone to pull him back. But, what if there was no one to pull him back next time?

"It was just a dream, Raph," Raphael whispered. "Nothin's gonna happen."

He pushed away from the wall and headed back towards the lair. He didn't notice a figure move in the shadows. Soulless black eyes watched as the red masked turtle disappeared over the side of the roof. A dark grin crossed over the figure's lips.

"Found ya."

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Reviews are welcome, flames are not


	2. Chapter 2

**Disclaimer** : see chapter one

* * *

The old grandfather clock chimed midnight. Had he really been working that late? He should have been home hours ago, the store had closed at ten. The watch maker finished up the pocket watch he was fixing and put everything away. He walked out into the main part of the store and noticed a light flashing on the phone. He pressed the button and the automated voice stated that he had one new voice message. The phone beeped and a familiar voice sounded from the speaker.

It was his most mysterious customer, Donatello. He had done business with The Shadow, as he called him, on several occasions. They never met face to face. Donatello would call with special orders for parts and when they were complete, the shipment was placed by the back door in the alley. The watch maker listened to the message, writing down the new shipment order, underlining Donatello's name twice and putting down urgent in capital letters.

The message ended and the phone beeped again. The watch maker played the message again to make sure he had the order right before erasing the message. He would get to work on the order first thing in the morning, just as soon as he got some sleep. Yawning deeply, the watch maker made his way into the back room again. He frowned, not remembering turning off the lights. He reached over and flipped the switch. The room was empty.

Suddenly, a large, strong hand shot around his mouth. He cried out, hands shooting to the one around his mouth. His heart plummeted into his stomach. What the hell? The hand only had three fingers. He reached up, grabbing a piece of fabric. There was a growl and whatever had a hold of him pulled away. The fabric tore in his hand. He looked down at the dark red cloth. An arm wrapped around his body.

There was the sickening crunch of bones shattering as the watch maker's neck was snapped. The man's body collapsed to the floor, eyes wide and fearful. The red masked turtle grinned darkly as he made his way to the back door. Before he left he tripped the alarm. The cops should show up any minute. And, hopefully, so would the Turtles.

* * *

Blue eyes gazed down at the lifeless body of Peter Conroy. He was the best watch maker in Brooklyn. The guy was a saint, not even so much as a parking ticket. So, why, detective Casey Jones had to wonder, did anyone want to kill the guy? CSU was combing out front for any prints. So far, all they found was a note for an order written by Conroy himself. The order had been for Donatello. There was only one Donatello that Casey knew of in New York, and he had to wonder if some enemy of the Turtles had found out about the business deal between Conroy and Donatello, and in some twisted sense of revenge, killed Conroy to get to them.

Casey knew it was a long shot guess, but he could never tell with the Turtles. Even two years after meeting them, he still felt like he was living a waking dream. It hadn't just been April O'Neil who T-boned his existence on that fateful night. His existence had been derailed as soon as the Turtles showed up the first time when Shredder escaped police custody. If Casey knew one thing about the Turtles, it was that they certainly knew how to make an entrance.

Casey knelt down beside the body, eyes scanning for anything out of the ordinary. His gaze fell on a piece of red fabric that was clenched in the man's hand. Pulling on gloves, Casey pried the piece of fabric out of the man's stiff fingers. He knew that shade of red anywhere. To anyone else it was just a normal piece of red fabric, but to Casey it was a major blow to the gut.

"He couldn't have," the detective whispered to himself. "Why would Raph..."

Casey shook his head. He couldn't go jumping to conclusions based on one piece of red cloth. There was no way Raphael would do something like this. He was a crime fighter, a ninja. Honor bound to uphold the moral code. Not to mention, Casey had become close friends with the red masked turtle over the years. It seemed their anger issues had given them some common ground.

Casey stood up when his cell phone started to ring. He put the cloth in an evidence bag and pulled off his gloves, taking out his cell phone and opening it. He placed the phone to his ear.

"Detective Jones," he answered.

"Never going to get used to hearing that," came the reply.

"Donnie?" Casey whispered, looking around the room to see if anyone listening in.

"Who else would it be?" Donatello asked. "Or did you forget that you left a message for me to call you?"

Casey felt his face burn with embarrassment. "Sorry. Got caught up in something."

"What's up?" Donatello asked. "What can this lowly sewer dweller do for New York's top detective?"

Casey's face burned hotter. "Not quite there, yet, Donnie," he said in a low voice.

"Don't be so humble, Casey," Donatello told him. "You've put away some pretty dangerous criminals."

"And he didn't even have to wear his hockey mask," Raphael's voice sounded in the background. "How's the head, pretty boy?"

"Shut up, Raph. Adults are talking," Donatello said. "So, what can I do for you?"

Casey looked down at the clear plastic bag in his hand. "Actually, Donnie..." He took a breath. "It's about Raph."

In the lair, Donatello fell forward in his chair. "What about Raph?" he asked, scared of the answer.

Hearing his name, Raphael turned to look at his brother. He frowned slightly when he saw the nervous look on Donatello's face.

"Has he been with you all night?" Casey asked.

Donatello swallowed nervously, eyes locking with his red masked brother's gaze. Raphael gave him a questioning shrug.

"Not...all night," Donatello answered truthfully. "He went out for an hour or so earlier to get some air."

"Did you notice anything...off about him?" Casey asked.

"Casey, you're scaring me. What do you think Raph did?" Donatello questioned.

Raphael walked up. "What do you mean, 'What Raph did'?" he asked.

"I don't know," Donatello answered.

"Do you know a guy by the name of Peter Conroy?" Casey asked.

"Conroy? Yeah, he gives me parts for inventions," Donatello replied.

"He was murdered tonight," Casey declared.

Horror destroyed any calm that Donatello was trying to portray. "M-murdered?" he stammered.

"And he was holding a piece of red cloth," Casey continued. "Now, that's a little suspicious since the guy owns a clock shop with not a piece of fabric in sight."

"Hold on a second," Raphael said, leaning in close to Donatello's phone. "You think I killed someone? Just because the guy was holding a red cloth?"

"I'm hoping it's not you, okay, Raph? I really don't want to be the guy who drags a giant, six foot tall turtle in for murder," Casey said.

Raphael backed away slightly. "Fair enough," he stated more calmly.

"But, I'm still gonna need to see your mask, Raph," Casey replied. "Just to be safe."

Raphael growled low in his throat, but a pointed look from Donatello made him swallow it.

"Fine," the hot-head spat.

"I'm almost done here. I'll be by when I'm finished," Casey told the brothers.

"Alright. See you soon," Donatello said before hanging up.

Raphael stalked away, huffing loudly. Donatello couldn't imagine what was going through his brother's head at that moment. To be accused of murder...and by his own friend. It was no wonder Raphael had almost lost his cool. However, Casey would come down and he would see that there was nothing out of the ordinary, that everything was fine and Raphael did not commit any crime.

Raphael pounded away at his punching bag. His knuckles burned with every punch. He tried to convince himself that Casey was wrong to accuse him of murder. Though, deep down, he secretly feared that Casey was right, and that he _had_ killed that man. The image of his nightmare self flashed in his mind's eye. What if he was losing himself to his demons? What if he _had_ killed Peter Conroy? Was it possible to do something and not remember doing it?

Raphael stood still, his arms by his sides and the punching bag swinging gently on its chain. His eyes were locked on the floor, mind searching for anything that would give him some clarity to what Casey had just told them. Raphael removed his mask and held it in his hands. Conroy had been found holding a piece of red cloth. Raphael turned the mask in his hands, only one tail fell down. He had lost the other one during a topside training spar with Leonardo earlier that night. Or had he? Did he just dream up the spar to give himself an alibi for what he had really done? Raphael clenched the mask in his hands, swallowing thickly. Was he a killer?

He couldn't even trust his own memories anymore.

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Reviews are welcome, flames are not


	3. Chapter 3

**A/N** : Thanks to everyone who has read and reviewed thus far. I hope you're enjoying the story.

 **Disclaimer** : see chapter one

* * *

Casey examined the mask in his hands. There was nothing special about it, it was just a piece of red cloth. The air in the lair was thick with tension. He could practically feel the nervousness radiating from Raphael. He couldn't blame his friend. If their roles were reversed, Casey was sure he would be just as nervous.

"What happened to your mask?" Casey asked. "It's missing a tail."

Raphael swallowed thickly. "I uh..."

"That was my fault," Leonardo spoke up, making Casey look up. "We were sparring and I swung at Raph's head. He ducked and I ended up slicing off a piece of his mask."

Casey nodded. "Okay," he said. He handed the mask back to Raphael. "Sorry about the suspicion, Raph."

Raphael took the mask back and put it on. "You're just doin' your job," he said.

"Still. I don't like suspecting my friends of murder," Casey explained. "I became a detective to put real criminals away, not the innocent."

"The NYPD is lucky to have you, Casey," Leonardo said. "You fought hard to get here."

Casey smiled. "Yeah, well, it took a while since my credibility came into question because of four certain turtles, though," he joked.

"Our bad," Michelangelo piped up.

"But, it all worked out, in the end," Donatello put in.

Casey chuckled. "Again, thanks to you guys." He checked his watch. "I'd best be getting topside," he said. "I have a dead body and no suspects."

"Good luck," Leonardo told him.

Casey waved over his shoulder as he headed out of the lair. Raphael's shoulders visibly dropped as he sighed heavily with relief. Leonardo patted him on the shoulder.

"Thanks, Leo," Raphael whispered.

"I simply told him the truth," Leonardo said.

"Still," Raphael muttered. "Saved my shell."

He turned and headed off towards the weight room. The others watched his retreating back with curious worry.

"Does Raph seem...off to anyone?" Michelangelo asked, his voice low.

"Yeah," Donatello agreed. "He could have easily told Casey about the spar, but it was like his brain just shut down."

Leonardo sighed in worry. "Something's going on. I know there's something else that's bothering him. I just don't know what that is."

"Raph's always been guarded," Donatello said. "It's nothing new."

"Except he told me that he has nightmares about the first time we faced off against Shredder," Leonardo confessed.

Donatello's eyes widened in surprise. Michelangelo frowned.

"Raph has nightmares?" the youngest asked.

"Who would've guessed?" Donatello mumbled.

Leonardo looked between his brothers. "Something's going on with Raph. And whatever that something is, it's breaking down his walls."

"It's possible. When people are in distress they seem to gravitate towards those closest to them," Donatello said. "Maybe that's why he opened up to you about his nightmares."

Leonardo crossed his arms, shifting on his feet. "If anything I've only ever driven Raph away," he muttered. "Why would he come to me when Master Splinter could help him so much more?"

"Only Raph can answer that, unfortunately," Donatello replied.

Leonardo lowered his gaze to the floor. He hoped his hot-headed brother was okay. The turtle with the black eyes flashed in his mind's eye. Leonardo rubbed his shoulder absent mindedly. Was the turtle just a figment of his overworked mind? Or was the dream actually a vision? Leonardo had read countless books about the possibility of seeing visions, but he never put any stock in them. Yes, he meditated to focus his mind, but it was more of a stress relief than seeking inner enlightenment.

"I guess we'll never know, then," Michelangelo's voice broke Leonardo out of his thoughts.

"Maybe, maybe not," Donatello said. "Only time will tell."

Leonardo gazed up towards the weight room. The rattling of the weights echoed down from high above. What was going on with their brother? Leonardo wondered if Raphael was having the same dreams he was having. But, how was that possible? Although, it was the only explanation he could come up with.

"I'm going to talk to Master Splinter," Leonardo said. "I'll see you guys later."

He walked off, leaving his siblings to do their own thing. He stepped up to Splinter's bedroom door and knocked softly. A gentle voice bid him to enter. Leonardo opened the door and entered the room. Splinter was sitting in the middle of the room, legs crossed and eyes closed. Leonardo closed the door and quietly walked over to sit down in front of his father.

"You are troubled," Splinter stated without opening his eyes.

Leonardo nodded, even though he knew Splinter couldn't see it. "I am," he confirmed.

Splinter opened his eyes and looked at his eldest son. "What troubles you, my son?"

"A number of things," Leonardo replied.

"Name one," Splinter instructed.

Leonardo took a breath before speaking. "The first is Raph. He's been acting strangely lately."

Splinter nodded as he listened. "Go on."

"Earlier tonight, he came to check on me, saying that I was crying out in my sleep," Leonardo explained. "Then, he confessed to me that he has nightmares about losing me, Donnie and Mikey to Shredder."

"A rare thing for him to say," Splinter commented, processing the information. "What else?"

Leonardo shifted, trying to get more comfortable. "Just then, when Casey was here asking about his whereabouts this evening, it was like he couldn't remember...or rather, he couldn't trust his memories."

"What happened?" Splinter asked.

"I told Casey that Raph was with me. I told him that we were sparring earlier tonight," Leonardo answered. "Casey accepted it and apologized to Raph for suspecting him of murder."

"An honorable thing to do, admitting one's mistakes," Splinter said. "And where is Raphael, now?"

"In the weight room," Leonardo replied.

Splinter hummed in thought and nodded. "What else has been troubling you? Besides your brother."

Leonardo inhaled deeply and slowly released it. "I keep having these dreams," he began. "I'm standing on the edge of the Chrysler Building. I'm all alone and I have no weapons and no way to contact the others. It's then that I discover the Technodrome is assembling, even though I know we defeated Krang and sent him and the Technodrome back through the portal. Then, I hear a scream. I turn and see April hanging off the side of the building. But, when I go to help her, I hear my brothers call for me."

Leonardo could feel his hands begin to shake as he recalled the dream. Splinter could see his son's distress. He reached out and put a hand on Leonardo's shoulder.

"Go on," Splinter coaxed.

"I turn again, but it's just as Krang throws Raph off the platform. All I can do is watch in horror as Raph plummets towards the ground. April screams for me again, but I know I can only help one. It's either her...or my brothers. A voice sounds behind me, confirming my horror. I turn around and see a turtle that looks like Raph standing behind me. Though he looks like Raph, he isn't. Even though he has Raph's face and build, his eyes are wrong. They're a deep, soulless black. When I ask him who he is, he always says he's the one I couldn't save. He continues to say that I can only save one, either April or my brothers, and yells at me to choose. I wake up when he pushes me off the Chrysler Building and I land on a panel of the Technodrome."

Leonardo exhaled heavily, his shoulders feeling lighter after confessing about the dream. Splinter hummed again and pulled his hand away, his fingers going to his chin. Leonardo looked up, his blue eyes questioning.

"What does it mean, Dad?" he asked, his voice no more than a whisper.

He could almost see the gears turning in Splinter's mind. He hoped beyond hope that his father knew something about this other turtle; if he was real or just a figment in a dream.

"Could it be..." Splinter mumbled under his breath. His ears twitched.

"What is it?" Leonardo asked.

"It's not possible," Splinter whispered.

"What's going on, Dad?" Leonardo questioned.

Splinter shook his head. "No. It's nothing. I just...need to meditate on the matter further."

Leonardo nodded. "Alright," he said before getting to his feet.

Splinter watched as his son walked out of the room and closed the door. He looked down at the floor, his eyes haunted. How was it possible? It couldn't be true. Splinter closed his eyes and took several deep breaths.

 _There had been only four,_ he told himself. _There had been only four._

If there had been another, then one of his sons had perished in that fire.

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Reviews are welcome, flames are not


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